The Republican Party’s civil war finally arrived, and it isn’t over yet.

The candidate who boasted she had castrated hogs won the Republican Senate primary in Iowa Tuesday, and in the bitter Mississippi GOP primary race, it might just come to that. The fight in the Magnolia State has been ugly, weird, full of old grudges and fault lines, and new national rancor over the soul of the Republican Party. Now the contest has been thrown into a three-week runoff.

John Dickerson is a Slate political columnist, the moderator of CBS’s Face the Nation, and author of Whistlestop and On Her Trail.

Incumbent Sen. Thad Cochran received 48.9 percent of the vote Tuesday and his Tea Party challenger, state Sen. Chris McDaniel won 2,000 more votes to earn 49.6 percent. In Mississippi, if no candidate gets 50 percent of the vote, a run-off follows.

That six-term Sen. Thad Cochran is in such trouble is a sign of how much politics has changed in the Tea Party era, and more proof that those grassroots conservative forces are healthy. In some states, like North Carolina and Georgia, GOP candidates have appealed to Tea Party voters and won despite the opposition of Tea Party elites who have backed other candidates. In Nebraska a Tea Party candidate won, but his credentials and political skill made him acceptable to establishment figures who want to win above all else. In Iowa, primary victor Jodi Ernst was supported by movement conservative organizations as well as the Chamber of Commerce.

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During the entire GOP primary season, much has been made about the brewing civil war within the Republican Party. But the races up until Tuesday managed, for a variety of reasons, to tamp down those differences. On Tuesday in Mississippi, the battle was joined. The clash between ideology and pragmatism there has been more pronounced than anywhere else, but it has been playing out through a distinctly local filter.

There is nothing personally objectionable about the 76 year-old Cochran. Quite the opposite: courtly, kindly, and gentlemanly are a part of his clamshell packaging. He is an incumbent in a business where incumbents almost always get elected. And what would seem to make him healthier than Bob Bennett of Utah and Dick Lugar of Indiana—incumbents who lost to Tea Party–backed candidates in the last election cycle—is that if Cochran is re-elected he will have considerable power in a possible Republican Senate majority. His position on the Appropriations Committee could translate into money for his state that benefits more than others from the federal budget.

If the Mississippi race is an archetypal Tea Party vs. establishment showdown, it also contains plenty of local spice.

Republican incumbents like Sens. Orrin Hatch, Mitch McConnell, and Lindsey Graham learned to reshape themselves in the era of Tea Party threats, but that's not what Cochran has done. He has been running as a man who has delivered for the state in the past—on everything from the farm bill to funding in the wake of Hurricane Katrina—and will deliver in the future.

That very power, which used to make incumbents nearly invincible, is part of what made him vulnerable. McDaniel says that Cochran, once referred to as “King of the Earmarks,” is just the kind of politician who has grown the federal government and lost touch with the state’s conservative principles.

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In the various GOP primaries we've seen this cycle, many of the fights have seemed contrived, but this one has the elements of a serious ideological debate about the size and role of government. Political scientists David Corbin and Matt Parks write about the Mississippi contest in the Federalist, saying that "talk about restoring constitutional government is just that—until voters are willing to give up their place at the pork-barrel trough."

But if the Mississippi race is an archetypal Tea Party vs. establishment showdown from one angle, it also contains local spice—yet another warning against trying to neatly fit any race and its candidates into a pundit Mad Lib. The final weeks of the contest have been dominated by a bizarre back and forth over a surreptitious photograph taken of Cochran's wife, Rose, who lives in a nursing home where she has suffered from dementia for 14 years. The incident, chronicled by my colleague David Weigel, led to the arrest of McDaniel supporters and Tea Party activists. It was the fallout of a long-standing campaign by the candidates' supporters to inject questions about Cochran's fidelity to his wife into the bloodstream of the race. (Cochran shares a house with his assistant, Kay Webber, and travels regularly with her.)

This episode led to an attack on McDaniel's character and counter-claims from McDaniel, who denies any involvement (and hasn't been linked to it). He and his aides say it is the Cochran campaign that is abusing the invalid Rose Cochran.

The race at times has had the feeling of a hijacking. Cochran, who has been on a sort of high-stakes amble across the state in recent weeks, doesn't really seem to have his heart in it. He wanted to retire but was pushed to run again, say local insiders, because friends and allies implored him—he could do so much for the state given his seniority. As Cochran has hit the stump—the first time he has really had to actively campaign since 1984—the insistent claims by his supporters that he is campaigning vigorously only hangs a lamp on the fact that this is a campaign of a man from another generation who has had jumper cables hooked to him.

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Cochran's campaign has taken its toughness not from its genteel pinstripe-wearing candidate, but from local operatives who have been savaging McDaniel as unprincipled, untrustworthy and a tool of outside groups like the Club for Growth and the Senate Conservative Fund. It's not just the nursing home scandal, they insist, it's that McDaniel is slippery, shifting his positions on Common Core, tort reform, and federal aid for Hurricane Katrina victims. (Fact checks here and here.)

McDaniel, almost half Cochran's age, is a hard-charging former talk show host who has welcomed outside forces who want to make him the sign of a Tea Party that is still alive and kicking. Sarah Palin and Rick Santorum campaigned for him in the final week, championing his support for "constitutional government" against the "old guard." They have a justified reason to celebrate their blow to the old-line GOP.

“They just want a scalp,” says Haley Barbour, former two-term governor, whose nephews Austin and Henry are heavily involved in the contest. “These outside groups don't care about Mississippi. They don't know Pascagoula from Pelahatchie. They just want a victory for their national political reputation.” That message isn't limited to Mississippi alone. The Republican Main Street Partnership, which is on the other side of the ideological battle from Tea Party groups, has tried to raise questions about candidate's local credentials when they have been supported by outside groups.

In Mississippi both sides have benefited from outside help. Cochran's campaign raised about $3.6 million for the race; McDaniel's $1.2 million. But outside interests injected $8 million, including $4.5 million for McDaniel and $3.2 million for Cochran.

What will those outside groups do now? Cochran will have a harder time in a run-off because McDaniel's troops are more committed and more likely to turn out for that vote in three weeks. His out-of-state donors, known for their passion, will be doubly so. Given that, the forces of pragmatism that have been backing Cochran have a dilemma. Do they keep supporting Cochran and attacking McDaniel, or do they step back, given that McDaniel could be the party's nominee and Democrats are anxious to use an ugly battle to tar the party more broadly? That might be the prudent thing to do, and a source in one big-money group that could help Cochran says they’re not going to because the writing is on the wall. American Crossroads says it will not interfere in the race. The Chamber of Commerce, which has backed Cochran, will continue to do so, says a source, but the level of that future commitment has yet to be determined.

Meanwhile, Henry Barbour, who runs the local super PAC helping the incumbent, seems ready for a fight. He tweeted, “There will be a heavy reload on both sides…This race is about MS's interests vs outside groups who've hijacked the Tea Party & their flawed candidate.” But what about the candidate himself? Cochran sure doesn't seem jazzed about wading even deeper into the Mississippi mud.